Series 1: The Use of <i>hsp</i>65- and <i>erm</i>(41)-Targeted Amplicon Sequencing in the Diagnostic Workflow for Non-Tuberculous Mycobacteria
Evolving technologies available to clinical laboratories and laboratory-related updates to clinical guidelines both drive the need for clinical laboratories to keep their test menu updated and in line with current technological and clinical developments. Our laboratory has developed a targeted Illum...
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| Format: | Article |
| Language: | English |
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MDPI AG
2025-07-01
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| Series: | Tropical Medicine and Infectious Disease |
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| Online Access: | https://www.mdpi.com/2414-6366/10/7/192 |
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| author | Tracy Lee Adriana Cabrera Kathleen Kolehmainen Trevor Hird Danielle Jorgensen Alan O’Dwyer Dan Fornika Rupinder Kaur KhunKhun Mabel Rodrigues Natalie Prystajecky John Tyson Inna Sekirov James E. A. Zlosnik |
| author_facet | Tracy Lee Adriana Cabrera Kathleen Kolehmainen Trevor Hird Danielle Jorgensen Alan O’Dwyer Dan Fornika Rupinder Kaur KhunKhun Mabel Rodrigues Natalie Prystajecky John Tyson Inna Sekirov James E. A. Zlosnik |
| author_sort | Tracy Lee |
| collection | DOAJ |
| description | Evolving technologies available to clinical laboratories and laboratory-related updates to clinical guidelines both drive the need for clinical laboratories to keep their test menu updated and in line with current technological and clinical developments. Our laboratory has developed a targeted Illumina-based amplicon next-generation sequencing (NGS) assay to interrogate the <i>hsp</i>65 and <i>erm(</i>41) genes of <i>Mycobacterium</i> spp. for the purposes of providing species-level ± subspecies-level identification of <i>Mycobacterium</i> spp. organisms in clinical samples and genotypic predictions for inducible macrolide resistance (in the case of <i>M. abscessus</i> complex members). The developed assay demonstrated 100% sensitivity and specificity for <i>M. tuberculosis</i> and <i>M. abscessus</i> complex cultured organisms, 98% ID overall concordance relative to the available reference identification, and a nearly 60% “rescue” rate for primary samples that could not be identified using our previous method. There was 94.6% concordance between genotypic and phenotypic results for inducible macrolide resistance. The developed assay was successfully implemented in our clinical laboratory and has been accredited for clinical use. |
| format | Article |
| id | doaj-art-63ad3b7155864b4d9770da1f4faaf7f5 |
| institution | DOAJ |
| issn | 2414-6366 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Tropical Medicine and Infectious Disease |
| spelling | doaj-art-63ad3b7155864b4d9770da1f4faaf7f52025-08-20T02:47:10ZengMDPI AGTropical Medicine and Infectious Disease2414-63662025-07-0110719210.3390/tropicalmed10070192Series 1: The Use of <i>hsp</i>65- and <i>erm</i>(41)-Targeted Amplicon Sequencing in the Diagnostic Workflow for Non-Tuberculous MycobacteriaTracy Lee0Adriana Cabrera1Kathleen Kolehmainen2Trevor Hird3Danielle Jorgensen4Alan O’Dwyer5Dan Fornika6Rupinder Kaur KhunKhun7Mabel Rodrigues8Natalie Prystajecky9John Tyson10Inna Sekirov11James E. A. Zlosnik12British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, CanadaBritish Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, CanadaBritish Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, CanadaBritish Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, CanadaBritish Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, CanadaBritish Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, CanadaBritish Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, CanadaBritish Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, CanadaBritish Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, CanadaBritish Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, CanadaBritish Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, CanadaBritish Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, CanadaBritish Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, CanadaEvolving technologies available to clinical laboratories and laboratory-related updates to clinical guidelines both drive the need for clinical laboratories to keep their test menu updated and in line with current technological and clinical developments. Our laboratory has developed a targeted Illumina-based amplicon next-generation sequencing (NGS) assay to interrogate the <i>hsp</i>65 and <i>erm(</i>41) genes of <i>Mycobacterium</i> spp. for the purposes of providing species-level ± subspecies-level identification of <i>Mycobacterium</i> spp. organisms in clinical samples and genotypic predictions for inducible macrolide resistance (in the case of <i>M. abscessus</i> complex members). The developed assay demonstrated 100% sensitivity and specificity for <i>M. tuberculosis</i> and <i>M. abscessus</i> complex cultured organisms, 98% ID overall concordance relative to the available reference identification, and a nearly 60% “rescue” rate for primary samples that could not be identified using our previous method. There was 94.6% concordance between genotypic and phenotypic results for inducible macrolide resistance. The developed assay was successfully implemented in our clinical laboratory and has been accredited for clinical use.https://www.mdpi.com/2414-6366/10/7/192non-tuberculous mycobacteriaidentificationspeciationnext-generation sequencingmolecular resistance |
| spellingShingle | Tracy Lee Adriana Cabrera Kathleen Kolehmainen Trevor Hird Danielle Jorgensen Alan O’Dwyer Dan Fornika Rupinder Kaur KhunKhun Mabel Rodrigues Natalie Prystajecky John Tyson Inna Sekirov James E. A. Zlosnik Series 1: The Use of <i>hsp</i>65- and <i>erm</i>(41)-Targeted Amplicon Sequencing in the Diagnostic Workflow for Non-Tuberculous Mycobacteria Tropical Medicine and Infectious Disease non-tuberculous mycobacteria identification speciation next-generation sequencing molecular resistance |
| title | Series 1: The Use of <i>hsp</i>65- and <i>erm</i>(41)-Targeted Amplicon Sequencing in the Diagnostic Workflow for Non-Tuberculous Mycobacteria |
| title_full | Series 1: The Use of <i>hsp</i>65- and <i>erm</i>(41)-Targeted Amplicon Sequencing in the Diagnostic Workflow for Non-Tuberculous Mycobacteria |
| title_fullStr | Series 1: The Use of <i>hsp</i>65- and <i>erm</i>(41)-Targeted Amplicon Sequencing in the Diagnostic Workflow for Non-Tuberculous Mycobacteria |
| title_full_unstemmed | Series 1: The Use of <i>hsp</i>65- and <i>erm</i>(41)-Targeted Amplicon Sequencing in the Diagnostic Workflow for Non-Tuberculous Mycobacteria |
| title_short | Series 1: The Use of <i>hsp</i>65- and <i>erm</i>(41)-Targeted Amplicon Sequencing in the Diagnostic Workflow for Non-Tuberculous Mycobacteria |
| title_sort | series 1 the use of i hsp i 65 and i erm i 41 targeted amplicon sequencing in the diagnostic workflow for non tuberculous mycobacteria |
| topic | non-tuberculous mycobacteria identification speciation next-generation sequencing molecular resistance |
| url | https://www.mdpi.com/2414-6366/10/7/192 |
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